Theme B: B1 Molecules - B1.2 Proteins

Question 1

order of a protein formation

Answer 1

amino acid –> dipeptide molecule –> polypeptide (protein)

Question 2

essential amino acids

Answer 2

can NOT be synthesised and must be obtained from food. includes 9/20 of the different amino acids. NOT required to give examples of essential and non essential amino acids.

Question 3

why is there a huge variety of polypeptides possible?

Answer 3

a) DNA codes for the number and order of amino acids within polypeptides
b) There are 20 different amino acids
c) Polypeptides can vary in length, from a few to thousands of amino acids
d) Some polypeptides are modified by cells after initial synthesis
e) Amino acids can be arrange in any order

although each polypeptide synthesised by the same gene turns out identical, there’s an immense number of gene and amino acid combinations that lead to an almost infinite number of possible permutations meaning that different polypeptides can have specific functions.

Question 4

common structure of a amino acid

Answer 4

amine functional group (NH2) on left, R group on top centre, carboxyl (COOH) functioning group on right, hydrogen bottom centre, all around one carbon.

Question 5

how are dipeptide molecule formed

Answer 5

word equation:
amino acid 1 + amino acid 2 –> dipeptide + water

the water moleucle formed form the hydroxyl group (-OH) of the carboxyl group of amino acid 1 and a hydorgen ion (H+) from amino acid 2. this frees up electrons to be shared between the carbon and nitrogen atoms. a new covalent bond called a peptide bond bonds the two to form a dipeptide

Question 6

examples of common polypeptides

Answer 6

Haemoglobin: oxygen-carrying protein in red blood cells
Keratin: in hair nails, claws, and hooves
Lipase: digestive enzyme that helps hydrolyse ingested lipids
Collagen: in connective tissue like tendons and ligaments
Histones: proteins in the nucleus of a cell that help form chromatin and chromosomes
Insulin: hormone that helps regulate blood sugar

Question 7

denaturation

Answer 7

**Denaturation is the process in which a protein or enzyme loses its three-dimensional structure due to the disruption of bonds, rendering it biologically inactive.
**
Causes:
* Placed in an a environment at a temperature above their physiological optimum
* pH levels that are not close to optimum pH
* Chemicals (e.g., heavy metals or detergents)

Mechanism:
* The increased molecular motion buts a lot of stress on the relatively weak bonds/forces (e.g., hydrogen bonds, ionic bonds) stabilising the protein’s tertiary and secondary structure, leading them to be broken.
* The primary structure (sequence of amino acids) remains intact.

• as long as the bonds between amino acids remain intact, the protein will return to its normal shape and function. pH denaturation is usually reversible as long as underlying peptide chain is not damaged, however most heat-induced denaturation is irreversible.

Question 8

R-groups

Answer 8

r-groups determine the properties of assembled polypeptides: they make them different from each other and create unique strutters and characteristics for specific proteins.

R-groups have hydrophilic or hydrophobic properties:

there are 9 non polar amino acids, their R-group is only hydrocarbon

there are 6 polar amino acids, their R group contains elements that form a polar covalent bond (O, N, or S)

there are 2 amino acids that are polar due to ionisation charge (-), their R-group acts as an acid.

there are 3 amino acids that are polar due to ionisation charge (+), their R-group acts as a base.

Question 9

acidic and basic R groups

Answer 9

in most organisms, amino acids are typically in a neutral or aqueous solution where both the amine and carboxyl group ionise. this happens because the carboxyl group acts as an acid and donates a hydrogen ion, while the amine group acts as a base and accepts a hydrogen ion. results in carboxyl group having a net negative charge and the amine group having a net positive charge.

Acidic R-Groups: Found in amino acids with R-groups containing a carboxyl group (-COOH). The carboxyl group can lose a hydrogen ion (H⁺), becoming negatively charged (-COO⁻).

Basic R-Groups: Found in amino acids with R-groups containing an amine group (-NH₂). The amine group can gain a hydrogen ion (H⁺), becoming positively charged (-NH₃⁺).

Question 10

primary structure of a protein

Answer 10

the number and sequence of amino acid held togetehr by peptide bonds (essentially a polypeptide chain). this seuqence is determined by a gene. the DNA sequence in the gene will be translated into the same sequence of amino acids (the same primary strcuture) each time, making proteins precise, repeatable and predictable despite their complexity. there will always by an unbonded amine group and an unbonded carboxyl group.

Question 11

secondary structures of proteins

Answer 11

Secondary Structures:
* Beta-Pleated Sheet
* Alpha Helix

Key Points:
* These structures are stabilized by hydrogen bonds between non-adjacent amine (H) and carboxyl (O) groups.
* Oxygen atoms have a partial negative charge, and hydrogen atoms have a partial positive charge.
* Non-polar R-groups do not directly affect secondary structures, allowing the backbone to fold freely into alpha-helices or beta-pleated sheets.
* Polar R-groups can form additional interactions (e.g., hydrogen bonds) but usually influence the overall folding at the tertiary level rather than the secondary structure itself.

Properties:
* The only way for hydrogen bonds to form is for the chain to adopt an alpha helix or beta-pleated sheet structure.
* Proteins with purely these shapes lack a unique, complex globular shape.
* Are relatively insoluble and often form fibrous proteins with structural roles related to movement.

Note:
Alpha helices and beta sheets can also be incorporated into larger, more complex globular proteins.

Question 12

bonding interactions that can occur between amino acids at the tertiary level (to form tertiary strcutures)

Answer 12

1) ionic bonds
2) hydrophobic interactions
3) disulfide bonds
4) hydrogen bonds

Question 13

ionic bonds (tertiary strcture)

Answer 13

Ionised R-groups (some negatively charged, some positively charged) can align to form ionic bonds. For example:

• Acidic R-Groups: Amino acids with a carboxyl group (-COOH) in their R group lose a hydrogen ion (H⁺), becoming negatively charged (-COO⁻).
• Basic R-Groups: Amino acids with an amine group (-NH₂) in their R group gain a hydrogen ion (H⁺), becoming positively charged (-NH₃⁺).
• The oppositely charged R-groups are then attracted to each other, forming a stable ionic bond.

Question 14

hydrophobic interaction

Answer 14

non polar amino acids are hydrophobic, and will fold into an area within the interior of the polypeptide in an attemot to avoid the polar water molecules. this is known as a hydrophobic interatcion.

Question 15

disulfide bond

Answer 15

• The strongest bonding force influencing polypeptide shape.
• Formed between cysteine amino acids within a polypeptide chain.
• Each cysteine’s R-group contains a sulfur atom bonded to a hydrogen atom (-SH).
• When two adjacent cysteine residues come close, the hydrogen atoms are removed, allowing the sulfur atoms to form a covalent bond between each other.
• This resulting bond is known as a disulfide bond.
• Disulfide bonds help stabilize the tertiary and quaternary structure of proteins.

Question 16

hydrogen bonds

Answer 16

polar amino acids will form hydrogen bonds with each other and are often on or near the exterior of the polypeptide because of tehir hydrophilic properties. Hydrogen bonds are typically the most numerous.

Question 17

solubility of proteins with non polar amino acids

Answer 17

proteins made of non polar amino acids have poor solubility in the cytoplasm and other aqueous solutions. they’re primarily structural proteins that are generally stationary and thus do not need to be soluble.

Question 18

solubility of proteins made of polar amino acids

Answer 18

proteins with polar amino acids have much better solubility and are often found in different location within the cell of body. Solubility allows these proteins to perform roles in the cytoplasm, bloodstream, or other water-based environments

Question 19

lipase (e.g. of proetin with interesting solubility)

Answer 19

Function:
Lipase is an enzyme that catalyzes the hydrolysis of lipid molecules.

Structure and Solubility:
The primary structure of lipase enables folding into a shape with a high concentration of hydrophobic amino acids in the enzyme’s core to interact with the lipid substrate.
Hydrophilic amino acids are located on the enzyme’s surface, allowing it to be soluble in an aqueous environment.

Overall Structure:
Lipase has a tertiary globular shape, with regions of alpha helix and beta-pleated sheet structures contributing to its stability and function.

Question 20

glycoprotein A & B solubility (e.g. of proetin with interesting solubility)

Answer 20

Glycoproteins A and B are proteins found on the membranes of red blood cells and determine the ABO blood type.

Structure and Solubility:
The protein portion of these glycoproteins embeds itself into the phospholipid bilayer of the membrane, with a portion extending into the blood plasma.
To stay embedded in the membrane, non-polar (hydrophobic) amino acids of the protein interact with the hydrophobic interior of the membrane.
The folding of the protein also places polar (hydrophilic) amino acids in contact with the sugar component of the glycoprotein, allowing interactions with the aqueous blood plasma.

Question 21

quaternary structure of a protein

Answer 21

2 or more amino acid chains bonded together into a single molecular strcture.

Question 22

insulin (as an example of a protein with quaternary structure)

Answer 22

Function:
* Insulin is a protein hormone secreted by the pancreas that promotes glucose uptake by body cells.

Structure:
* Initially synthesized as a single chain of 110 amino acids in pancreatic cells.
* Modified within the pancreas to form two chains:
* One chain with 21 amino acids.
* Another chain with 30 amino acids.
* These two chains are held together by three disulfide bonds, resulting in a 51-amino-acid functional structure.

Quaternary Structure:
* Insulin is inactive in pancreatic cells because it forms dimers (two insulin molecules temporarily bonded together).
* Three dimers can further associate to form a hexamer.
* These dimers and hexamers represent quaternary structures used for storage in the pancreas.
* Upon secretion, insulin separates into its monomer form, becoming active as a hormone.

Question 23

collagen (e.g. of quaternary structure)

Answer 23

most abundant protein in the human body. its makes up the connective tissue, provides tensile strnegth to tendons, ligaments and gives elastcitiy to skin

collagen is a fribrous protein consisting of 3 polypeptide chains wound aroynd each other in a helix shape. this arrangement gives collagen its quarternary structure.

Question 24

haemoglobin

Answer 24

rleatively large protein in our red blood cells which reversibly bind to oxygen in th elungs and carry oxygen to body tissue where its released for aerobic cell respiration. can also bind reversibly to CO2 to be taken out of body.

an example of a conjugated quaternary strcyture which exhbitis each type of protein strcture:
1) Primary Structure
The sequence of amino acids in each of the four polypeptide chains (two alpha and two beta subunits).
2) secondary structure
Alpha-helices and beta-pleated sheets form within each polypeptide chain due to hydrogen bonding between amino acids. These structures contribute to the overall folding of each chain.
3) Tertiary Structure
Each polypeptide chain folds into a globular shape, stabilized by hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bonds. The three-dimensional shape enables the binding of oxygen to the iron-containing heme group.
4) quaternary strcture
Four subunits (two alpha and two beta chains) come together to form the functional hemoglobin molecule.

Question 25

non conjugated proteins

Answer 25

Proteins made entirely of amino acids, without any non-protein components (prosthetic groups) attached.

Question 26

conjugated proteins

Answer 26

the proetin has one or more non proteins groups as part of the molecule (the haem group in haemoglobin.)

Question 27

haem group

Answer 27

A prosthetic group (non-polypeptide component) found in hemoglobin that is responsible for binding oxygen.
Structure:
Composed of an iron (Fe²⁺) atom at the center of a porphyrin ring.
The iron atom can form coordinate bonds with oxygen molecules, allowing oxygen to bind and be transported.
Function:
Each of hemoglobin’s four subunits contains one heme group, allowing it to carry up to four oxygen molecules.
The heme group is essential for hemoglobin’s ability to pick up oxygen in the lungs and release it in tissues that require oxygen.

Question 28

gloular proteins

Answer 28

Definition: Proteins with a compact, spherical shape formed by the folding of polypeptide chains into a tertiary or quaternary structure. they have very specialised roles

Properties:
Soluble in water due to hydrophilic R-groups on the outside and hydrophobic R-groups in the core.

example: insulin (a hormone)
* released into the bloodstream after blood glucose levels rise ( like after a meal or snack with carbs)
* the bloodstream takes insulin to all body cells. each cell has membrane proteins called insulin recpetors.
* the insulin molecules firs perfectly into the insulin receptor when a set of reaction occur (called a signal pathway) whcich opens the chennals in teh plasma membrane allowing glucose to enter the cell.

Question 29

fibrous proteins

Answer 29

Definition: Proteins with a long, linear structure that form strong, insoluble fibers or sheets.

Properties:
Insoluble in water due to a high concentration of hydrophobic amino acids.
Provide structural support and strength in tissues.
Lack a compact tertiary structure; their primary and secondary structures dominate.

example: collagen
* amino acids within collagen are short repeating sequences of glycine - proline - X.
* X is a different amino acid depending on a location and specialised function of the collagen molecule
* repeating sequences provides very regular and fibrous shape
* structural uniformity if collagen makes it an excellet molecule for building tissues that hold the body together.